$\begingroup$This question is too broad. There are many available QC programs which all have their own advantages/disadvantages. Do you have a specific use case that you would like the QC to be applied to?$\endgroup$
– gringerJun 1 '17 at 2:05

1

$\begingroup$agree with @gringer. Right now the answer to this question is, roughly, whatever you get by googling 'NGS QC'. If you can provide a detailed use case - e.g. maybe you have 200GB of paired-end illumina data from 12 individuals of a non-model species, and you have a distant reference available - it will be a much more useful question and one that google couldn't solve.$\endgroup$
– roblanfJun 4 '17 at 10:30

We routinely run both FastQC and FastQ Screen on all of our raw sequencing reads. FastQ Screen is a tool for detecting cross-species contamination. MGA is another similar tool.

There are then lots of QC tools specific to different types of data, most of which run after alignment. For example RSeQC (RNA data), Qualimap and many many others. Without specifying what kind of data you have this is a bit difficult to make recommendations for though.

The quality control of ngs reads is heavily dependent on type of the project.

For genome assembly projects based on short reads, beside already covered checking quality of sequencing, you would like to look at the kmer spectra to find out, if your reads are going to make sense when they will be translated to De Brujin graph. You will get also a clues about genome coverage, genome size, repetitive content and small clue about heterozygocity. A lot of useful info about interpretation you can find in the README of GenomeScope.

If you are looking for NGS QC for your fastq, bam, bed and vcf files I would suggest a commercial tool called omnomicsQ.

It automates coverage analysis and sample pass, warn fail according according to your defined SOPs. Unlike fastqc it also comes with a database so that you can compare protocols, samples, and your performance to peer organisations. It also charts performance over time, exceptions,and correlations between metrics